DimPlot(obj.srt, group.by = 'sample', alpha = 0.8) + 
  scale_color_paletteer_d("ggsci::nrc_npg") + theme_bw()

DimPlot(obj.srt, group.by = 'sample', 
        split.by = 'sample', ncol = 2, alpha = 0.5) +
  scale_color_paletteer_d("ggsci::nrc_npg") + theme_bw()

obj.srt@meta.data %>% ggplot(aes(sample, fill=sample)) + 
  geom_bar(alpha=0.7, color="grey5", size=0.1) +
  geom_text(stat="count", aes(label= ..count..), vjust=-0.5, size=3) +
  xlab("") + 
  theme_classic() +
  theme(legend.title = element_blank(),
        axis.text.x = element_text(angle = 45, vjust=0.5)) 

# Resolution and color palette
i=1
res= paste0("RNA_snn_res.", resolution_values[i])
palette <- wesanderson::wes_palette("FantasticFox1", length(levels(obj.srt@meta.data[,res])), type = "continuous")

DimPlot(obj.srt, group.by = res, cols = palette, alpha = 0.8) + 
  theme(plot.title = element_blank()) + xlab("UMAP1") + ylab("UMAP2")

DimPlot(obj.srt, group.by = res, alpha = 0.8,
        label = T, label.box = T, label.size = 3, cols = palette) + theme(plot.title = element_blank())

obj.srt@meta.data %>% ggplot(aes(!!sym(res), fill=!!sym(res))) + 
  geom_bar(alpha=0.7, color="grey5", size=0.1) +
  geom_text(stat="count", aes(label= ..count..), vjust=-0.5, size=3) +
  scale_fill_manual(values=palette) + 
  xlab("") + 
  theme_classic() +
  theme(legend.title = element_blank(),
        axis.text.x = element_text(angle = 0, vjust=0.5)) +
  ggtitle("Number of genes by Cluster")

obj.srt@meta.data %>% ggplot(aes(sample, fill=!!sym(res))) +
  geom_bar(position = "fill", color="grey9",size = 0.2) +coord_flip() +
  theme_bw() + 
  theme(legend.title = element_blank()) +
  scale_fill_manual(values=palette) +xlab("") +ylab("Fraction") 

obj.srt@meta.data %>% ggplot(aes(!!sym(res), fill=sample)) + 
  geom_bar(position = "fill", color="grey9",size = 0.2, alpha=0.8) + scale_fill_paletteer_d("ggsci::nrc_npg") + theme_classic()+ 
  theme(legend.title = element_blank()) +
  ylab("Fraction")

# Resolution and color palette
i=2
res= paste0("RNA_snn_res.", resolution_values[i])
palette <- wesanderson::wes_palette("FantasticFox1", length(levels(obj.srt@meta.data[,res])), type = "continuous")

DimPlot(obj.srt, group.by = res, cols = palette, alpha = 0.8) + 
  theme(plot.title = element_blank()) + xlab("UMAP1") + ylab("UMAP2")

DimPlot(obj.srt, group.by = res, alpha = 0.8,
        label = T, label.box = T, label.size = 3, cols = palette) + theme(plot.title = element_blank())

obj.srt@meta.data %>% ggplot(aes(!!sym(res), fill=!!sym(res))) + 
  geom_bar(alpha=0.7, color="grey5", size=0.1) +
  geom_text(stat="count", aes(label= ..count..), vjust=-0.5, size=3) +
  scale_fill_manual(values=palette) + 
  xlab("") + 
  theme_classic() +
  theme(legend.title = element_blank(),
        axis.text.x = element_text(angle = 0, vjust=0.5)) +
  ggtitle("Number of genes by Cluster")

obj.srt@meta.data %>% ggplot(aes(sample, fill=!!sym(res))) +
  geom_bar(position = "fill", color="grey9",size = 0.2) +coord_flip() +
  theme_bw() + 
  theme(legend.title = element_blank()) +
  scale_fill_manual(values=palette) +xlab("") +ylab("Fraction") 

obj.srt@meta.data %>% ggplot(aes(!!sym(res), fill=sample)) + 
  geom_bar(position = "fill", color="grey9",size = 0.2, alpha=0.8) + scale_fill_paletteer_d("ggsci::nrc_npg") + theme_classic()+ 
  theme(legend.title = element_blank()) +
  ylab("Fraction")

## sankey plot 
library(ggsankey)
library(ggplot2)
library(dplyr)

cols = c('sample','RNA_snn_res.0.2','RNA_snn_res.0.4')
data =obj.srt@meta.data[, cols]

# Function to create a Sankey plot
create_sankey_plot <- function(data, column_names, title, show_labels = FALSE){
  df <- data %>%
    make_long(!!column_names[1], !!column_names[2], !!column_names[3])
  
  dagg <- df %>%
    group_by(node) %>%
    tally()
  
  df2 <- merge(df, dagg, by.x = 'node', by.y = 'node', all.x = TRUE)
  
  pl <- ggplot(df2, aes(x = x,
                        next_x = next_x,
                        node = node,
                        next_node = next_node,
                        fill = factor(node),
                        label = paste0(node," n=", n))
  )
  
  pl <- pl + geom_sankey(flow.alpha = 0.5, color = "gray40", show.legend = show_labels)
  if (show_labels) {
    pl <- pl + geom_sankey_label(size = 3, color = "white", fill = "gray40", hjust = 1)  # Change hjust value to 1 (right-aligned)
  }
  
  pl <- pl + theme_bw()
  pl <- pl + theme(legend.position = "none")
  pl <- pl + theme(axis.title = element_blank(),
                   axis.text.y = element_blank(),
                   axis.ticks = element_blank(),
                   panel.grid = element_blank())
  pl <- pl + scale_fill_viridis_d(option = "plasma")
  pl <- pl + labs(title = "")
  
  pl <- pl + labs(fill = 'Nodes')
  
  return(pl)
}

# Assuming obj.srt@meta.data is your data and you want to use specific columns for the Sankey plot
column_names <- cols

# Create the Sankey plot using the specified columns
sankey_plot <- create_sankey_plot(data = obj.srt@meta.data, column_names, 
                                  title = "", show_labels = TRUE)

# Display the plot
print(sankey_plot)